The first part of this review focused on the skeletal aspects of vitamin D. This second part reviews some of the available evidence that vitamin D may have a physiological extraskeletal role beyond its traditional effect on the skeleton. This aspect has influenced the definition of vitamin D deficiency and what level of vitamin D should be regarded as optimal. The recognition of the prevalence of vitamin D deficiency and insufficiency has led to debate as to whether and how we should be treating asymptomatic individuals. This review discusses the potential extraskeletal effects of vitamin D, the definition of vitamin D deficiency and our thoughts on indications for measurement and treatment.