Introduction This study was motivated by the report that infant development correlates with particular lipids in infant plasma. Objective The hypothesis was that the abundance of these candidate biomarkers is influenced by the dietary intake of the infant. Methods A cohort of 30 exclusively-breastfeeding mother–infant pairs from a small region of West Africa was used for this observational study. Plasma and milk from the mother and plasma from her infant were collected within 24 h, 3 months post partum. The lipid, sterol and glyceride composition was surveyed using direct infusion MS in positive and negative ion modes. Analysis employed a combination of univariate and multivariate tests. Results The lipid profiles of mother and infant plasma samples are similar but distinguishable, and both are distinct from milk. Phosphatidylcholines (PC), cholesteryl esters (CEs) and cholesterol were more abundant in mothers with respect to their infants, e.g. PC(34:1) was 5.66% in mothers but 3.61% in infants (p = 3.60 × 10−10), CE(18:2) was 8.05% in mothers but 5.18% in infants (p = 1.37 × 10−11) whilst TGs were lower in mothers with respect to their infants, e.g. TG(52:2) was 2.74% in mothers and 4.23% in infants (p = 1.63 × 10−05). A latent structure model showed that four lipids in infant plasma previously shown to be biomarkers clustered with cholesteryl esters in the maternal circulation. Conclusion This study found evidence that the abundance of individual lipid isoforms associated with infant development are associated with the abundance of individual molecular species in the mother’s circulation.