The understanding, identification, quantification and control of impurities in drug substances are essential as new molecular entities are evaluated in clinical development. As chemical processes used to produce drug substances mature from the early phases of development through registration, a concomitant maturing of process-related impurity understanding and control is required. This paper outlines strategies available to pharmaceutical scientists to aid in that understanding. Methodology aspects for impurity investigations are discussed along with an emphasis on understanding the origin and fate of impurities to guide decisions on process controls and specifications. Orthogonal analytical approaches for impurity investigations to provide a complete understanding of a drug substance impurity profile and to aid chemical process development are described. Special considerations necessary for stereochemical impurity investigations are also discussed. Considerations for control of toxic impurities include sensitive and selective analytical methodology and determination of the process capability for removing the impurity. A case study is given where routine analytical testing for a toxic impurity was not required because a high impurity rejection efficiency of the synthetic process was demonstrated. Quality assessment of starting materials from multiple sources and the impact of starting material impurities on the impurity profile of the drug substance are discussed with illustrative examples. Knowledge gained from these investigations provides a sound basis for setting specifications for impurities in key starting materials.