A systematic and efficient methodology for conceptual design of mechanisms is developed based on the classification of design specifications. In this work, design specifications for a mechanism are recast into three more coherent categories: functional requirements, structural requirements and design constraints. Based on functional requirements, the functioning kinematic chain of the mechanism is constructed by the functioning links such as the ground, input and output links, etc. According to structural requirements, kinematic structures are searched from the existing atlas of kinematic structures. Then, the functioning kinematic chain is compared with segments of the kinematic structures searched to obtain a much smaller number of compatible kinematic structures, where development of conceptual design of mechanisms can be efficiently accomplished. Lastly, joints of the compatible kinematic structures are labeled subject to design constraints, such that feasible mechanisms are yielded. With this methodology, design specifications with different natures can be used to guide a designer through various stages of the conceptual design process in a systematic manner. The creation of the variable-stroke engine mechanism is used as an illustrative example. Two design examples, the creation of the latch and retainer mechanisms for wafer containers are presented to demonstrate the proposed methodology. It is believed that the proposed methodology and design examples are beneficial to the conceptual design of mechanisms.