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Background/aims: Long-chain polyunsaturated fatty acids (LC-PUFA) are regarded as essential for child cognition. Genetic variation in fatty acid (FA) desaturase enzyme (FADS) has been recognized as an important effect modifier in the relation between LC-PUFA and child cognitive function. This study aimed to identify the distribution of genetic variant (genotype) SNP rs174468 and to assess plasma FA and developmental outcome by the genotype among under-2 year old Sasaknese Indonesian children., Methods: Data was collected at baseline of a randomized trial (NUPICO, clinicaltrials.gov NCT01504633) in East Lombok district, Indonesia. Breastfed, 12- 17 month old children were recruited and 240 subjects were included in the study. Child cognition was assessed as Bayley Mental Developmental Index (MDI)., Results: From 206 subjects whose blood samples can be collected, only two genotypes were found (90.3% GG homozygotes, 9.7% AG heterozygotes), and minor allele AG was significantly associated with higher level of arachidonic acid (20:4 n-6), n-6 LC-PUFA and FADS1 index. MDI score was associated with a FADS2 index (DHA:EPA ratio) but not genotype (Adjusted R-square= 0.043)., Conclusions: FADS2 index was associated with cognitive function. No difference was found between children with GG and AG genotypes who were all breastfed and not low birth weight.