Growth patterns are known to differ between breastfed and formula-fed infants, but little is known about the relative impact of maternal smoking in pregnancy v. feeding mode on growth trajectory in infancy. We conducted a secondary analysis of a trial, the Tolerance of Infant Goat Milk Formula and Growth Assessment trial involving 290 healthy infants, to examine whether smoking in pregnancy modified the association between feeding mode and body composition of infants. Fat mass (FM) and fat-free mass (FFM) were estimated at 1, 2, 3, 4, 6 and 12 months of age using bioimpedance spectroscopy. Formula-fed infants (n 190) had a higher mean FFM at 4 months (mean difference (MD) 160 g, 95 % CI 50·4, 269·5 g, P < 0·05)) and 6 months (MD 179 g, 95 % CI 41·5, 316·9 g, P < 0·05) compared with the breastfed infants (n 100). Sub-group analysis of breastfed v. formula-fed infants by maternal smoking status in pregnancy showed that there were no differences in the FM and FFM between the breastfed and formula-fed infants whose mothers did not smoke in pregnancy. Formula-fed infants whose mothers smoked in pregnancy were smaller at birth and had a lower FM% and higher FFM% at 1 month compared with infants of non-smoking mothers regardless of feeding mode, but the differences were not significant at other time points. Adequately powered prospective studies with an appropriate design are warranted to better understand the relative impact of maternal smoking, feeding practice and the growth trajectory of infants.