The absence of a standardized classification of hypospadias hinders understanding of the anatomic differences among patients and the evaluation of outcomes following surgical repair. In working towards a standardized, objective method of recording patients' hypospadias anatomy, we describe our initial experience using a non-invasive three-dimensional scanner. An Artec3D Space Spider scanner was used to obtain 3D scans in 29 patients undergoing hypospadias repair. Measurements of the urethral plate width, urethral plate length, glans width, penile shaft length, and penile shaft width were made by 2 pediatric urology attendings and 1 pediatric urology fellow. Measurements were compared and inter-rater reliability was calculated. A total of 435 measurements were made on 29 successfully generated 3D scans, ranging from distal to proximal hypospadias. The inter-rater reliability of measurements from the generated 3D models shown good inter-rater reliability of urethral plate width (ICC0.87 [95%CI:0.76,0.93]), penile shaft length (ICC0.87 [95%CI:0.70,0.94]) and glans width (ICC0.83 [95%CI:0.68,0.92]), excellent inter-rater reliability of urethral plate length (ICC0.96) and moderate inter-rater reliability of penile shaft width (ICC0.69 [95%CI:0.44,0.84]). There was a high degree of reliability of measurements made across multiple users. Calculation of the ratio of the urethral plate length/total penile shaft length objectively defined the initial position of the urethral meatus. When compared to the 3-dimensional volume of the glans, a more proximally positioned urethral meatus was associated with a lower glans volume. 3D scanning offers a rapid, reproducible, and non-invasive method of documenting hypospadias anatomy. The ability to evaluate three dimensional features (i.e. glans volume) offers an exciting opportunities for robust investigation of hypospadias outcomes and further understanding of the relationship between a patient's genotype and phenotype.