Although innate lymphoid cells (ILCs) have recently been identified also in skin, their role in this organ remains poorly understood. In this study, we aimed at developing a technique to assess ILCs in situ and to determine their topographical distribution in human skin. We collected lesional skin biopsies from patients with atopic dermatitis and psoriasis (both n = 13) and normal human skin from healthy controls. After establishing immunofluorescence ILC in situ stainings, we developed an analysis approach (gating combined with manual validation) to reliably identify ILCs. Topographical mapping was obtained by automated calculations of the distances between ILCs and different cellular/structural elements of the skin. Whereas normal human skin harbored a very scarce ILC population (mostly ILC1s and AHR+ILC3s), atopic dermatitis and psoriasis skin was infiltrated by clearly visible ILC subsets. We observed atopic dermatitis skin to contain not only ILC2s but also a prominent AHR+ILC3 population. Conversely, we encountered almost equal proportions of ILC1s and RORC+ILC3s in psoriasis skin. Distance calculations revealed ILCs to reside near the epidermis and in close proximity to T lymphocytes. ILC mapping in situ will provide valuable information about their likely communication partners in normal and diseased skin and forms the basis for the appropriate mechanistic studies.