At our institution, the techniques that technicians use for health checks vary for mice housed in cages on individually ventilated caging (IVC) racks. If the mice cannot be adequately visualized, some technicians partially undock the cage whereas others use an LED flashlight. These actions undoubtedly alter the cage microenvironment, particularly with regard to noise, vibration, and light, which are known to affect multiple welfare and research-related parameters in mice. The central aim of this study was to assess the effects of partial cage undocking and LED flashlight use during daily health checks on fecundity, nest building scores, and hair corticosterone concentrations in C57BL/6J mice to determine the least disturbing method of performing these health checks. In addition, we used an accelerometer, a microphone, and a light meter to measure intracage noise, vibration, and light under each condition. Breeding pairs (n = 100 pairs) were randomly assigned to one of 3 health check groups: partial undocking, LED flashlight, or control (in which mice were observed without any cage manipulation). We hypothesized that mice exposed to a flashlight or cage undocking during daily health checks would have fewer pups, poorer nest building scores, and higher hair corticosterone levels than did the control mice. We found no statistically significant difference in fecundity, nest building scores, or hair corticosterone levels between either experimental group as compared with the control group. However, hair corticosterone levels were significantly affected by the cage height on the rack and the amount of time on study. These results indicate that a short duration, once-daily exposure to partial cage undocking or to an LED flashlight during daily healthy checks does not affect breeding performance or wellbeing, as measured by nest scores and hair corticosterone levels, in C57BL/6J mice.