The present work proposes a design procedure along with guidelines for the choice of initial clearance of a typical rotating gas turbine seal in a secondary air system. The basis for the design is to prevent seal rubbing against stator, by ensuring that the centrifugal and thermal growths of the seal are within the safe operating limits. As a case study, a six-tooth straight-through rotating labyrinth seal configuration is considered with wide ranging seal parameters, namely the seal inner radius (25–700 mm), speed (1000–5000 rad/s), temperature (200–650 ℃) and pressure ratio (1.1–2.5). By means of an iterative process, which involves computational fluid dynamics and finite element analysis techniques, and with a choice of initial clearance, an extensive database is generated. The results are presented in terms of non-dimensional variables, namely seal clearance ratio, centrifugal growth ratio, thermal growth ratio, operating clearance ratio due to centrifugal growth and operating clearance ratio due to thermal growth. It is found that the value of clearance ratio depends significantly on the dimensionless radial position. For a seal clearance ratio of 0.01, at 3000 rad/s, the leakage flow rate gets reduced by 18 and 4%, respectively for pressure ratios of 1.1 and 2.5, when the centrifugal growth alone is considered. When both centrifugal and thermal growths are considered, the percentage reduction becomes about 70% for the same seal operating at 3000 rad/s and 204 ℃, and it is as high as 95% at 426 ℃.