Microgravity (microG) is known to influence cytoskeletal structure, but its effects on cell migration are not well understood. To examine the effects of altered gravity on neural crest cell (NCC) migration, we inserted Xenopus laevis embryos into two separate microG-simulating slow turning lateral vessels (STLVs) just before neurulation (stage 11-12), and exposed them until feeding stage (stage 45), when the jaws and branchial apparatus are fully functional. To evaluate apparatus-related artifacts, we used two different STLVs and a vibration control as well as a stationary control vessel. Larval growth, pattern of NCC-derived cartilage formation, and incidence of malformations were analyzed using immunolocalization and wholemount staining of cartilage with Alcian blue. Interestingly, the two STLVs often yielded different or conflicting results. Many differences, such as increased cartilage size, attenuated Hoxa2 expression, and increased cell division, may be attributed mainly to vibration of the rotating vessels. However, tadpoles that developed in simulated microgravity (both STLVs, but not the vibration control) showed significantly more skeletal abnormalities, with stronger effects on cartilages derived from NCCs than those derived mainly from mesoderm. We conclude that migrating NCCs of Xenopus are sensitive to the altered gravitational environment of STLVs, and that studies relying on bioreactors to simulate microgravity also need to take variation in apparatus into account.