Flowcytometric analysis is widely used in characterization of stem cells. In areas where flowcytometry is not available, characterization of stem cells can be done using immunocytochemistry. This study aimed to compare the results of flowcytometry against immunocytochemistry for the measurement of CD34, CD73 and CD90 in stem cells. Adipose tissue derived stem cells were analyzed for their CD34, D73 and CD90 simultaneously, using a BD FACSCalibur flowcytometer (BD Biosciences) with 10,000 gated events. The same sample was made into spot specimens and checked for CD34, CD73 and CD90 by immunocytochemistry and when available, 100 cells were screened for positive results and percentages of positive results for CD34, CD73 and CD90 were computed. The results of the two methods were compared. Discrepancies between the two methods were noted for all samples. Discrepancies lower than 3, 11 and 11% for CD34, CD73 and CD90 respectively were regarded as agreement between the two methods. Percentages of agreement in CD34, CD73 and CD90 were calculated. Some spot specimens did not yield 100 cells and analyses were done on available cells. The agreement between the two methods for CD34, CD73 and CD90 were 22, 42 and 29% respectively. Agreement between flowcytometry and immunocytochemistry was low for CD34 and CD90 and was moderate for CD73.