Currently, various protocols regarding the site of waist circumference (WC) measurement are in place. This study aimed to analyse the effect of the site of WC measurement on visceral adipose tissue (VAT) estimation. WC was obtained at 7 anatomical sites in 211 German volunteers (103 males) aged 23–81 years using three-dimensional photonic body scanning (PBS). At one site, WC was additionally measured by tape. The quantity of VAT was assessed by MRI. Models to estimate VAT based on WC were developed; the precision of the estimation is represented by R2. The influence of the applied method of WC assessment (tape v. PBS) on the estimations is reported. Results show that the amount of estimated VAT and the precision of VAT estimation were dependent on the site of measurement. VAT was estimated most precisely by WC taken at the level of the lowest rib (WCrib: R2 = 0·75 females; 0·79 males), the minimum circumference (WCmin: R2 = 0·75 females; 0·77 males) and at the narrowest part of the torso (WCnar: R2 = 0·76 females; 0·77 males), and least precisely by WC assessed at the top of iliac crest (WCiliac: R2 = 0·61 females; 0·60 males). VAT estimates based on WC obtained by PBS were smaller and estimations were slightly less precise compared to estimates based on tape measures. Our results indicate that the method and the site of waist measurement should be considered when estimating VAT based on WC. The implementation of a standardised protocol using either WCrib, WCmin or WCnar could improve the precision of VAT estimation.