While undernutrition and anaemia have previously been linked to poor development of children, relatively little is known about the role of B-vitamins and fatty acids on cognition. The present study aims to explore the associations between indicators of body size, fatty acid and micronutrient status on cognitive performance in 598 Indian school children aged 6–10 years. Baseline data of a clinical study were used to assess these associations by analyses of variance adjusting for age, sex, school, maternal education and cognitive tester. The Kaufman Assessment Battery for Children II was used to measure four cognitive domains, including fluid reasoning, short-term memory, retrieval ability and cognitive speediness. Scores were combined into an overall measure, named mental processing index (MPI). Body size indicators and Hb concentrations were significantly positively related to cognitive domains and MPI, such that increases of 1 sd in height-for-age and weight-for-age z-scores would each translate into a 0·09 sd increase in MPI, P = 0·0006 and 0·002, respectively. A 10 g/l increase in Hb concentrations would translate into a 0·08 sd increase in MPI, P = 0·0008. Log-transformed vitamin B12 concentrations were significantly inversely associated with short-term memory, retrieval ability and MPI (β (95 % CI) = − 0·124 ( − 0·224, − 0·023), P = 0·02). Other indicators of Fe, iodine, folate and fatty acid status were not significantly related to cognition. Our findings for body size, fatty acids and micronutrients were in agreement with previous observational studies. The inverse association of vitamin B12 with mental development was unexpected and needed further study.