A proper understanding of the infection dynamics of influenza A viruses hinges on the availability of reliable estimates of key epidemiologic parameters such as the reproduction number, intrinsic growth rate, and generation interval. Often the generation interval is assumed to be similar in different settings although there is little evidence justifying this. Here we estimate the generation interval for stratifications based on age, cluster size, and social setting (camp, school, workplace, household) using data from 16 clusters of Novel Influenza A (H1N1) in the Netherlands. Our analyses are based on a Bayesian inferential framework, enabling flexible handling of both missing infection links and missing times of symptoms onset. The analysis indicates that a stratification that allows the generation interval to differ by social setting fits the data best. Specifically, the estimated generation interval was shorter in households (2.1 days [95% credible interval = 1.6–2.9]) and camps (2.3 days [1.4–3.4]) than in workplaces (2.7 days [1.9–3.7]) and schools (3.4 days [2.5–4.5]). Our findings could be the result of differences in the number of contacts between settings, differences in prophylactic use of antivirals between settings, and differences in underreporting.