The aim of the present study was to find out whether the incorporation of organic dairy and meat products in the maternal diet affects the contents of the conjugated linoleic acid isomers (CLA) and trans-vaccenic acid (TVA) in human breast milk. To this purpose, milk samples from 312 breastfeeding mothers participating in the KOALA Birth Cohort Study have been analysed. The participants had documented varying lifestyles in relation to the use of conventional or organic products. Breast milk samples were collected 1 month postpartum and analysed for fatty acid composition. The content of rumenic acid (the main CLA) increased in a statistically significant way while going from a conventional diet (no organic dairy/meat products, 0·25 weight % (wt%), n 186) to a moderately organic diet (50–90 % organic dairy/meat, 0·29 wt%, n 33, P = 0·02) and to a strict organic diet (>90 % organic dairy/meat, 0·34 wt%, n 37, P ≤ 0·001). The levels of TVA were augmented among the participants with a moderately organic diet (0·54 wt%) and those with a strict organic diet (0·59 wt%, P ≤ 0·001), in comparison with the conventional group (0·48 wt%). After adjusting for covariables (recruitment group, maternal age, maternal education, use of supplements and season), statistical significance was retained in the group of the strict organic dairy users (P < 0·001 for rumenic acid). Hence, the levels of CLA and TVA in human milk can be modulated if breastfeeding mothers replace conventional dairy and/or meat products by organic ones. A potential contribution of CLA and TVA to health improvement is briefly discussed.