Research procedures can have a detrimental effect on the reproductive success of the study species. In this study, the frequency of investigator disturbance on Short-tailed Shearwaters Puffinus tenuirostris was examined experimentally throughout the incubation period to assess whether disturbance influences hatching success, pre-fledging chick survival and chick body size. Handling of incubating birds every day, every 3 days and once a week reduced hatching success by 100, 61 and 39%, respectively, compared with pairs that were not disturbed. Most failures resulted from egg abandonment by the parents, particularly during the early stage of incubation. Chick survival did not differ between treatment groups, but control chicks were significantly heavier and had larger bill depths and longer wings. The difference in chick body mass and size observed between the control and disturbed chicks might be due to physiological or behavioural mechanisms in adults or carry-over effects from the incubation stage to the next life-history stage. Reduced offspring quality has the potential to affect post-fledging survival and recruitment. These findings are significant in broader terms because any investigator disturbance that reduces reproductive success, survival and offspring fitness could interfere with the accurate assessment of demographic parameters and exacerbate population declines.