Modelling human neurodevelopmental disorders is important in biomedical research since the brain cannot be easily accessed in humans. In this chapter, we describe a series of standardized procedures for the reliable analysis of neuroanatomical phenotypes (NAPs) of the adult mouse brain using quantitative 2D histological practices. Our goal is to provide the reader an experimental pipeline, ranging from experimental work through to data analysis, which can be performed in any academic research setting with or without access to a histology platform. Depending on the type of sections studied, parasagittal or coronal, the assessment of brain neuroanatomy is performed at stereotaxic sections, at Lateral +0.60 mm or at Bregma +0.98, −1.34 mm and −5.80 mm, respectively. A total of 118 neuroanatomical parameters made of brain areas and lengths can be quantified across these four defined sections, to characterize most brain regions involved in higher-order cognition such as the cortex, the hippocampus, the corpus callosum, and the cerebellum. The choice of these sections has been extensively validated for robustness in high-throughput projects aimed at characterizing brain NAPs in over 2000 mouse models of neurodevelopmental disorders.