To investigate the association of subcutaneous body fat levels in pregnant women with wheezing in their 18 month old infants. A prospective study of European and Polynesian volunteers (n = 369) recruited from northern New Zealand were visited in months 4 and 7 of pregnancy when height, weight, and triceps, biceps and costal skinfolds were measured, and questionnaires determining personal details administered; and again visited 18 months after birth when infants were measured and questions on infant feeding and wheeze administered. At 18 months 32 % of infants had wheezed in the past 12 months. Increased wheeze was associated with maternal asthma, eczema or allergy (p = 0.001); receiving family welfare payments (p = 0.010); and being Polynesian (p = 0.021); while exclusive breastfeeding to 2 months (p = 0.045) was associated with decreased wheeze. Individual month 4 and month 7 mean triceps, biceps and costal skinfolds were all greater in mothers of wheezers compared to nonwheezers, biceps and costal skinfolds significantly so (p = 0.002, p = 0.005 at month 7). The sum of these skinfolds at month 4, at month 7, and the difference between these sums, were all significantly associated with increased risk of infant wheeze at 18 months when considered alone (p = 0.037, p = 0.001 and p = 0.015) or in combination. Prevalence of infant wheeze was 22.7 % for mothers with lower quartile month 7 skinfolds, compared to 45.0 % for mothers with upper quartile. After adjusting for significant covariates the difference in skinfolds had the strongest association (p = 0.003) followed by sum at month 4 (p = 0.074 or 0.003 depending on whether Polynesian ethnicity was included in the model). The sum of skinfolds declined between month 4 and month 7 in 34 % of women. Prevalence of wheeze was 19.2 % where the difference in mothers' skinfolds between month 4 and month 7 decreased by 10 mm or more and 41.7 % where the difference increased by 10 mm or more. Mean month 4 weights, BMI and sum of skinfolds were below average in the latter group. As the sum of month 4 or month 7 maternal skinfolds increased the prevalence of infant wheeze increased. In addition as the change in skinfolds between month 4 and month 7 became more positive the prevalence of infant wheeze increased. This study suggests for the first time that changes in subcutaneous fat during pregnancy are associated with prevalence of infant wheeze.