Recent numerical studies in stratospheric dynamics and its variability as well as climate, have highlighted the need of more observational analyses to improve simulation of the West African monsoon (WAM). In this paper, activity and spectral characteristics of short-scale vertical waves (wavelengths <4 km) are analysed in equatorial coastal and tropical lower stratosphere during the WAM. A first detailed description of such waves over West Africa is derived from high-resolution vertical profiles of temperature and horizontal wind obtained during Intensive Observation Period of the African Monsoon Multidisciplinary Analyses (AMMA) Campaign 2006. Monthly variation of wave energy density is revealed to trace the progression of the inter-tropical convergence zone (ITCZ) over West Africa. Mesoscale inertia gravity-waves structures with vertical and horizontal wavelengths of 1.5–2.5 and 400–1100 km respectively and intrinsic frequencies of 1.1–2.2 f or periods <2 days are observed in the tropical LS with intense activity during July and August when the WAM is installed over the tropical West Africa. Over equatorial region, gravity waves with intrinsic frequencies of 1.4–4 f or periods <5.2 days, vertical wavelength of 2.1 km and long horizontal wavelengths of 1300 km are intense during the WAM coastal phase. From July to October, gravity waves with intrinsic frequencies of 1.2–3.8 f or periods <6 days, vertical wavelength of 2.1 km and horizontal wavelengths of 1650 km are less intense during the WAM Sahelian phase of the WAM, March–June. Unlike potential energy density, kinetic energy density is observed to be a good proxy for the activity of short-scale vertical waves during the WAM because quasi-inertial waves are dominant. Long-term wave activity variation from January 2001 to December 2009, highlights strong year-to-year variation superimposed on convective activity and quasi-biennial oscillation-like variations especially above tropical stations.