diff --git a/src/main/java/org/breedinginsight/brapps/importer/services/FileMappingUtil.java b/src/main/java/org/breedinginsight/brapps/importer/services/FileMappingUtil.java
index e26f375c5..e603a7d21 100644
--- a/src/main/java/org/breedinginsight/brapps/importer/services/FileMappingUtil.java
+++ b/src/main/java/org/breedinginsight/brapps/importer/services/FileMappingUtil.java
@@ -18,6 +18,7 @@
 package org.breedinginsight.brapps.importer.services;
 
 import io.reactivex.functions.Function;
+import org.apache.commons.collections4.map.CaseInsensitiveMap;
 import org.apache.commons.lang3.tuple.MutablePair;
 import org.apache.commons.lang3.tuple.Pair;
 import org.breedinginsight.brapps.importer.model.config.MappedImportRelation;
@@ -76,7 +77,7 @@ public List<Pair<Integer, String>> findFileRelationships(Table data, List<Mapped
     }
 
     public <T> List<T> sortByField(List<String> sortedFields, List<T> unsortedItems, Function<T, String> fieldGetter) {
-        HashMap<String, Integer> sortOrder = new HashMap<>();
+        CaseInsensitiveMap<String, Integer> sortOrder = new CaseInsensitiveMap<>();
         for (int i = 0; i < sortedFields.size(); i++) {
             sortOrder.put(sortedFields.get(i), i);
         }
diff --git a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
index c9e7f5aa0..66bc7db7e 100644
--- a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
+++ b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
@@ -24,6 +24,7 @@
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.collections4.map.CaseInsensitiveMap;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.v2.model.BrAPIExternalReference;
 import org.brapi.v2.model.core.*;
@@ -41,7 +42,6 @@
 import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
 import org.breedinginsight.brapps.importer.daos.*;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
-import org.breedinginsight.brapps.importer.model.base.AdditionalInfo;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
 import org.breedinginsight.brapps.importer.model.imports.PendingImport;
 import org.breedinginsight.brapps.importer.model.imports.experimentObservation.ExperimentObservation;
@@ -70,12 +70,9 @@
 import java.time.format.DateTimeFormatter;
 import java.time.format.DateTimeParseException;
 import java.util.*;
-import java.util.function.Function;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
 
-import static org.breedinginsight.brapps.importer.services.FileMappingUtil.EXPERIMENT_TEMPLATE_NAME;
-
 @Slf4j
 @Prototype
 public class ExperimentProcessor implements Processor {
@@ -444,10 +441,11 @@ private List<Trait> verifyTraits(UUID programId, List<Column<?>> phenotypeCols,
 
     private List<Trait> fetchFileTraits(UUID programId, Collection<String> varNames) {
         try {
+            Collection<String> upperCaseVarNames = varNames.stream().map(String::toUpperCase).collect(Collectors.toList());
             List<Trait> traits = ontologyService.getTraitsByProgramId(programId, true);
             // filter out just traits specified in file
             return traits.stream()
-                         .filter(e -> varNames.contains(e.getObservationVariableName()))
+                         .filter(e -> upperCaseVarNames.contains(e.getObservationVariableName().toUpperCase()))
                          .collect(Collectors.toList());
         } catch (DoesNotExistException e) {
             log.error(e.getMessage(), e);
@@ -547,8 +545,10 @@ private ValidationErrors validateFields(List<BrAPIImport> importRows, Validation
                                             List<Column<?>> phenotypeCols, boolean commit) throws MissingRequiredInfoException, ApiException {
         //fetching any existing observations for any OUs in the import
         Map<String, BrAPIObservation> existingObsByObsHash = fetchExistingObservations(referencedTraits, program);
-        Map<String, Trait> colVarMap = referencedTraits.stream().collect(Collectors.toMap(Trait::getObservationVariableName, Function.identity()));
-
+        CaseInsensitiveMap<String, Trait> colVarMap = new CaseInsensitiveMap<>();
+        for ( Trait trait: referencedTraits) {
+            colVarMap.put(trait.getObservationVariableName(),trait);
+        }
         Set<String> uniqueStudyAndObsUnit = new HashSet<>();
         for (int rowNum = 0; rowNum < importRows.size(); rowNum++) {
             ExperimentObservation importRow = (ExperimentObservation) importRows.get(rowNum);
@@ -619,7 +619,7 @@ private Map<String, BrAPIObservation> fetchExistingObservations(List<Trait> refe
                                    .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue));
     }
 
-    private void validateObservations(ValidationErrors validationErrors, int rowNum, ExperimentObservation importRow, List<Column<?>> phenotypeCols, Map<String, Trait> colVarMap, Map<String, BrAPIObservation> existingObservations) {
+    private void validateObservations(ValidationErrors validationErrors, int rowNum, ExperimentObservation importRow, List<Column<?>> phenotypeCols, CaseInsensitiveMap<String, Trait> colVarMap, Map<String, BrAPIObservation> existingObservations) {
         phenotypeCols.forEach(phenoCol -> {
             var importHash = getImportObservationHash(importRow, phenoCol.name());
             if(existingObservations.containsKey(importHash) && StringUtils.isNotBlank(phenoCol.getString(rowNum)) && !existingObservations.get(importHash).getValue().equals(phenoCol.getString(rowNum))) {
@@ -969,8 +969,10 @@ private void updateObservationDependencyValues(Program program) {
 
         // Update ObservationVariable DbIds
         List<Trait> traits = getTraitList(program);
-        Map<String, Trait> traitMap = traits.stream().collect(Collectors.toMap(TraitEntity::getObservationVariableName, Function.identity()));
-
+        CaseInsensitiveMap<String, Trait> traitMap = new CaseInsensitiveMap<>();
+        for ( Trait trait: traits) {
+            traitMap.put(trait.getObservationVariableName(),trait);
+        }
         for (PendingImportObject<BrAPIObservation> observation : this.observationByHash.values()) {
             String observationVariableName = observation.getBrAPIObject().getObservationVariableName();
             if (observationVariableName != null && traitMap.containsKey(observationVariableName)) {