The physiological condition of female birds during the egg-laying and incubation periods is of considerable interest and yet is relatively understudied in wild birds, primarily due to the difficulty of catching birds during this period without causing nest desertion. We therefore developed a box-net to capture cavity-nesting birds using sections of a mist-net placed around a metal cubic frame. We captured female Great Tits (Parus major) as they left nest boxes during the egg-laying and incubation periods and measured desertion rates. Using box-nets, we captured 108 of 119 (90%) females during egg laying and 10 of 12 (83%) during incubation. Our recapture rate over two consecutive days during incubation was 50% (5 of 10). Females not captured left nest boxes before we attempted to capture them, escaped through a hole in the mist-net, or remained in nest boxes for more than 2 h, after which we ended capture attempts. Overall, 22% of egg-laying females deserted, with desertion rates highest early in the egg-laying period. Desertion rates of females captured using box-nets did not differ from those of undisturbed females. One of 10 females captured in a box-net deserted during the incubation period. Box-nets are portable, can be set up and taken down quickly and easily, and could potentially be used with nest boxes or natural cavities at any height. Box-nets are easy to construct and adaptable for use with an array of cavity-nesting birds, and can be an important tool for studying female physiology during egg laying and incubation.