Recognizing that health outcomes are influenced by and occur within multiple social and physical contexts, researchers have used multilevel modeling techniques for decades to analyze hierarchical or nested data. Cross-Classified Multilevel Models (CCMM) are a statistical technique proposed in the 1990s that extend standard multilevel modeling and enable the simultaneous analysis of non-nested multilevel data. Though use of CCMM in empirical health studies has become increasingly popular, there has not yet been a review summarizing how CCMM are used in the health literature. To address this gap, we performed a scoping review of empirical health studies using CCMM to: (a) evaluate the extent to which this statistical approach has been adopted; (b) assess the rationale and procedures for using CCMM; and (c) provide concrete recommendations for the future use of CCMM. We identified 118 CCMM papers published in English-language literature between 1994 and 2018. Our results reveal a steady growth in empirical health studies using CCMM to address a wide variety of health outcomes in clustered non-hierarchical data. Health researchers use CCMM primarily for five reasons: (1) to statistically account for non-independence in clustered data structures; out of substantive interest in the variance explained by (2) concurrent contexts, (3) contexts over time, and (4) age-period-cohort effects; and (5) to apply CCMM alongside other techniques within a joint model. We conclude by proposing a set of recommendations for use of CCMM with the aim of improved clarity and standardization of reporting in future research using this statistical approach.