Introduction Deep vein thrombosis is a multifactorial disease with many acquired and genetic risk factors. Polymorphism in the APOE gene is an upcoming potential pathogenic factor whose role is unclear in deep vein thrombosis. Methods An equal number of deep vein thrombosis cases and controls (N = 100, each) were investigated for APOE gene polymorphisms along with known acquired and hereditable thrombophilic risk factors. APOE genotyping was done by polymerase chain reaction. Results The ε3/ε4 and ε2/ε3 APOE genotypes were commoner in deep vein thrombosis cases than controls but not statistically significant ( ε3/ε4 → 18% versus 11%, OR = 1.776, CI = 0.792–3.984, p = 0.16; ε2/ε3 →10% versus 9%, OR = 1.123, CI = 0.436–2.895, p = 0.809). However, the following risk factors were found to be laterally associated with APOE genotypes in cases of deep vein thrombosis: pregnancy with ε2/ε3 genotype positivity (N = 29; p = 0.019), recurrent pregnancy loss with ε3/ε3 genotype (N = 29; p = 0.016), normal antithrombin levels with ε3/ε3 genotype (N = 62; p = 0.03) and non-O blood group with ε3/ε4 genotype (N = 100; p = 0.023). Conclusion APOE genotypes have shown only a modest association with deep vein thrombosis and were not statistically significant. A lateral association of these genotypes with thrombophilic risk factors was observed which may be investigated further for the possible pathogenetic mechanisms and their therapeutic implications.