Beginning October 2015, the Center for Medicare and Medicaid Services will require medical providers to use the vastly expanded International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) system. Despite wide availability of information and mapping tools for the next generation of the ICD classification system, some of the challenges associated with transition from ICD-9-CM to ICD-10-CM are not well understood. To quantify the challenges faced by emergency physicians, we analyzed a subset of a 2010 Illinois Medicaid database of emergency department ICD-9-CM codes, seeking to determine the accuracy of existing mapping tools in order to better prepare emergency physicians for the change to the expanded ICD-10-CM system. We found that 27% of 1830 codes represented convoluted multidirectional mappings. We then analyzed the convoluted transitions and found that 8% of total visit encounters (23% of the convoluted transitions) were clinically incorrect. The ambiguity and inaccuracy of these mappings may impact the workflow associated with the translation process and affect the potential mapping between ICD codes and Current Procedural Codes, which determine physician reimbursement.