OBJECTIVES: To conduct a review of all recommendations made by NICE and the SMC up to June 2016 relating to submissions for treatments of rare diseases and to evaluate the impact of patient access schemes (PAS). METHODS: All appraisals made by NICE (single, multiple or highly specialised technology appraisals) and SMC evaluating drugs with an orphan drug designation by the EMA or treating a rare disease included on the Orphanet list of rare diseases were included in a database. Data on the intervention, comparator, therapeutic area as categorised by the British National Formulary (BNF), recommendation and incremental cost-effectiveness ratio (ICER) were extracted. Where a PAS was included, the type of PAS and the impact on the estimated ICER and final recommendation by NICE/SMC was also evaluated. RESULTS: NICE and the SMC appraised a total of 55 medicines with an orphan drug designation or that treated a rare disease. The most common therapeutic area was malignant disease and immunosuppression (66%), followed by nutrition and blood (7%) and respiratory (5%). Standard of care was the most common comparator. ICERs submitted by manufacturers to the SMC ranged from £21,454 to £184,513 and for NICE submissions from £13,472 to £45,499. Treatments receiving a positive recommendation either dominated the comparator or had ICERs below the traditional willingness-to-pay thresholds associated with NICE and the SMC. Subgroup analysis was often required to identify populations for whom the treatments were cost-effective. 30 submissions included a PAS, resulting in treatment being recommended for use in the majority of cases (22 out of 30). CONCLUSIONS: A review of recommendations made by NICE and the SMC for treatments of rare diseases showed that the evaluation of these treatments can present challenges when ascertaining if these treatments represent value-for-money. Including a PAS did not guarantee a positive recommendation by the reimbursement agency.