The histological characteristics of the gonads and paramesonephric ducts were investigated to allow a quantitative distinction among male, female, and intersex hatchling Green Sea Turtles (Chelonia mydas) from peninsular Malaysia. Hatchling sexes were identified initially as either males or females based on the incubation temperatures, and intersex hatchlings were collected from in situ nests. Traditionally, this assignment is confirmed by qualitative visual assessment of histological sections of the gonads and paramesonephric ducts. We describe a quantitative method for measuring these parameters to distinguish hatchling sex. The thickness of the paramesonephric duct epithelium area, the height of the nucleus in cells within the gonadal cortical epithelium, and the width of the gonadal ridge were measured in sections from 116 hatchlings. Upon examination of the histological material, hatchlings identified initially by incubation temperature as females were found to have significantly thicker paramesonephric duct epithelium and greater gonadal ridge width and cortical epithelium nuclear height compared with hatchlings identified as males. In addition, some hatchlings demonstrated histological characteristics of both sexes (designated here as intersex hatchlings) in some or all of the traditional histological sexing criteria. The “intersex” group could be divided into two subgroups by the quantitative measurements described here. Using this method, hatchlings could be classified as either males, females, or intersexes with a male-appearing gonad and female-appearing duct or a female-appearing gonad and male-appearing duct. The method outlined here provides a quantitative way to distinguish sex and provides insight in intersex grouping in hatchling C. mydas.