There are several techniques for estimating health state utility values, each of which presents pros and cons in the context of rare diseases (RDs). Direct approaches (e.g. standard gamble and time trade-off) may be too demanding for patients with RDs, since most of them affect young children or cause cognitive impairment. The alternatives are using “vignettes” that describe hypothetical health states for the general public, which may not reflect the heterogeneous manifestations of RDs, or multi-attribute utility instruments (i.e. indirect techniques), such as EQ-5D, which may be less sensitive in capturing the specificities of RDs. The “rule of rescue” approach is a promising alternative in RDs, since it prioritizes identifiable patients with life-threatening or disabling conditions. However, it raises measurement challenges and ethical issues. Furthermore, the literature reports on relevant implications of choosing a technique over others for health technology assessment, which should be considered in relation to individual RDs.