Current trends in quantitative health research have highlighted the inadequacy of the usual operationalisation of sex and gender, resulting in a growing demand for more nuanced options. This scoping review provides an overview of recent instruments for the operationalisation of sex and gender in health-related research beyond a concept of mutually exclusive binary categories as male or masculine vs. female or feminine. Our search in three databases (Medline, Scopus and Web of Science) returned 9935 matches, of which 170 were included. From these, we identified 77 different instruments. The number and variety of instruments measuring sex and/or gender in quantitative health-related research increased over time. Most of these instruments were developed with a US-American student population. The majority of instruments focused on the assessment of gender based on a binary understanding, while sex or combinations of sex and gender were less frequently measured. Different populations may require the application of different instruments, and various research questions may ask for different dimensions of sex and gender to be studied. Despite the clear interest in the development of novel sex and/or gender instruments, future research needs to focus on new ways of operationalisation that account for their variability and multiple dimensions.