Rotary engines require seals inserted into each rotor apex to maintain contact with the housing and prevent leaks during internal combustion. These seals are called apex seals and their effectiveness directly influences the engine operation and efficiency. The deviation function (DF) method of rotary engine design has several advantages over the conventional design method with regard to the apex seals, and also finds many more possibilities. The DF method can be used to incorporate the profile of the apex seal into the design process and the rotor profile itself. In the DF method, the seal profile is used as a generating curve and the housing bore profile is a generated curve. The housing is conjugate to the apex seal, and therefore conforms to the seal profile, unlike the conventional rotary engine. Another advantage the DF method has over the conventional method is that different apex seal profiles can be used, resulting in a larger variety of rotary engine designs. This paper introduces the DF method of rotary engine design and selection by the geometric parameters rotor radius, R, and eccentricity, l. In conventional rotary (Wankel) engine design, these parameters are used as a ratio called the K factor. The K factor uniquely identifies a conventional rotary engine profile and is therefore used to associate performance criteria such as displacement, compression ratio, and apex sealing. The DF method can be used to employ the same ratio as a selection tool. Instead of a single profile for each K factor, there is a range of possible DF-designed engine profiles associated with each R/l ratio. The resulting design flexibility is shown using two example deviation functions and the design criteria swept area and maximum theoretical compression ratio. Furthermore, the R/l ratio is not an indication of apex sealing effectiveness because the DF method of rotary engine design and selection separates the engine profile geometry from the apex seal geometry. An apex sealing index is presented to show how the DF method can be used to quantify, analyze, and improve apex sealing.