Abstract Background Obsessive compulsive disorder (OCD) has a complex etiology related to multiple neuropsychological factors. OCD is associated with several candidate genes but results are discordant. The objective was to explore the association between five polymorphisms related to neurotransmitters, the risk of an OCD diagnosis and the performance in four executive functions tests done with Colombian patients diagnosed with this condition. Methods 63 patients and 65 controls matched by gender and age were genetically analyzed. For the study of the relation between cognitive function and phenotypes, a subsample of 33 patients and 31 controls was used. The Stroop test, Wisconsin Card Sorting Test (WCST), Tower of London and Trail Making Test (TMT) for executive function assessment were applied and the SNPs analyzed were: COMT (rs4680), MAO-A (rs6323), HTTLPR (rs25531), HT2A (rs6315) and SLC1A1 (rs301434). Results Differences in the conceptualization of the WCST test (p = 0.023) and Stroop interference score (p = 0.041) between cases and controls were obtained. After analyzing the relationship between genotypes and sub-scores of the tests, associations between the presence of MAO-A, SLAC1A1, HTTLPR and HT2A alleles and tests sub-scores were found. Discussion This characterization of children with OCD is a new field of work in Colombia and one of the first works performed in Latin America. The sample size and the number of polymorphisms analyzed in this population should be increased.