We tested the association of four development-related gene polymorphisms with congenital anomalies. We assumed that those polymorphic variants may be a risk factor for developmental disorders. We analyzed 140 DNA samples isolated from archived paraffin tissue of deceased patients in whom fetal/neonatal autopsy examination had shown congenital malformations versus a control group of healthy children for four different polymorphisms: OSR1 rs12329305, rs9936833 near FOXF1, HOXA1 rs10951154 and MTRR rs326119. These polymorphisms were genotyped using the TaqMan allelic discrimination assay. Association analysis was performed on the allelic and genotypic distribution between the two tested groups. Significant allelic and genotypic association with stillborn/neonatal death was observed for rs12329305 (p=7×10-4, p=0.0013, respectively). In addition, association analysis for the same polymorphism was shown in the subgroup with isolated anomalies (p=1.25×10−5), particularly in the subgroup of cases with kidney and heart anomalies (p=4.18 x 10-5, p=5.12×10-8, respectively). Polymorphism rs9936833 near the FOXF1 gene showed only genotypic association with congenital malformations (p=0.034), when we compared minor allele heterozygotes and homozygotes versus major allele homozygotes, while the other two polymorphisms were not revealed. We also found that the OR for congenital malformations occurrence was 1.8 times higher in males than in females (p = 0.038), when we analysed the genotypic distribution of four examined polymorphisms along with sex. This is the first study, as far as we know, that showed the OSR1 gene polymorphism rs12329305 and rs9936833 near FOXF1, as well as male sex, are risk factors for different types of congenital malformations in cases of stillborn/neonatal death.