Health conditions known to affect this breed are , glaucoma, , and luxating patella.] Overall, however, they are of great genetic soundness and few Shibas are diagnosed with genetic defects in comparison to other dog breeds

Periodic joint examinations are recommended throughout life of the dog but problems are generally discovered early in the dog's life. Eye tests should be performed yearly as eye problems can develop over time. By two years of age, Shiba Inus can be considered fully free from joint problems if none have been discovered by this point, since at this age the skeleton is fully developed.

As with any dog, Shibas should be walked or otherwise exercised daily.