Short bowel syndrome (SBS) represents a serious intestinal absorption disorder, and patients may be prone to severe malnutrition. Dietetic therapy is critically important both for immediate prognosis and successful long-term rehabilitation. To maintain energy balance, an accurate assessment of energy intake is required. Our objective was to compare energy intake (EI) assessed by 24-h dietary recalls (EIrecall), a standard clinical assessment, with the total energy expenditure measured by the doubly labelled water (TEEdlw) method in SBS patients and matched controls. A total of twenty-two participants (eleven each in the SBS and control groups (CG), six female and five male) were evaluated; CG were matched to SBS patients on the basis of age, BMI and sex. TEE was measured by DLW and compared with EI determined by four 24-h dietary recalls using the USDA Automated Multiple-Pass Method. Bland–Altman plots and paired Student’s t test were used to compare EIrecall with TEEdlw (P<0·05). Participants’ mean age was 53 (sd 8) years. TEEdlw (7·85 (SD 1·16) MJ/d, 0·14 (SD 0·02) MJ/kg per d) was significantly lower (P=0·014) compared with EIrecall (11·07 (SD 3·45) MJ/d, 0·21 (SD 0·08) MJ/kg per d) in the SBS group. On the other hand, in the CG group TEEdlw (10·02 (SD 1·86) MJ/d, 0·18 (SD 0·03) MJ/kg per d) was significantly higher (P=0·001) compared with EIrecall (7·19 (SD 1·68) MJ/d, 0·13 (SD 0·03) MJ/kg per d). In SBS patients, reported EI is higher than DLW-measured EI. Therefore, providing or prescribing energetic intake based on EIrecall without accounting for potential malabsorption-related losses can compromise the energy needs in SBS patients and affect nutritional status in the long term.