Food safety is an important global public health and trade matter, with chemical hazards occupying centre stage due to associated acute and chronic health outcomes. There is also an increasing need to address antimicrobial resistance concerns. While food remains a major vehicle for exposure to these hazards, related matrices cannot be ignored. Animal feed for instance may contain drug or pesticide residues as well as mycotoxins that could carry-over to food either as parent compounds or their metabolites of toxicological relevance. Contaminated water is also another medium of potential exposure to food hazards. A concerted effort is required to address the need for a safe food supply and one critical stakeholder is the testing laboratory. While this requires trained and capable analysts as well as reliable instrumentation, analytical methods are a major need. Development and validation – to ensure fitness of purpose – and availability of these methods is a necessity. This manual, consisting of several Standard Operating Procedures (SOPs), presents another opportunity for laboratories to address gaps in analytical methods and/or expand their options. The manual contains techniques for analyzing certain mycotoxins such as aflatoxins, fumonisin and ochratoxin in matrices that include milk, edible vegetable oil and animal feed etc. A range of veterinary drug residues including permitted and prohibited substances in animal matrices including fish, are also addressed. Several pesticide residues in cereals, fruits and vegetables are also covered. A couple of methods for analysis of selected metals are also presented.