There is growing interest to constrain and validate greenhouse gas (GHG) emission inventories at urban and intra-urban scales. This contribution reviews methods to identify, quantify and attribute emissions (and sequestration) of carbon dioxide, methane and nitrous oxide in cities using in-situ measurements in the atmo- sphere. Measurements of GHG mixing ratios and fluxes in cities will allow validation of inventories, identification and quantifica- tion of poorly-known sources and accounting for the effects of urban land-cover change. In-situ measurements of GHG emissions (and sequestration) in the urban atmosphere are possible (i) at the micro-scale by capturing GHG plumes of individual sources using mobile platforms and measuring vertical profiles of GHGs in the urban canopy layer, (ii) at the local-scale by direct eddy-covariance flux measurements of GHGs on towers, and, (iii) at the meso-scale by measurements of mixing ratios and isotopologues of GHGs in the urban and rural boundary layer combined with box and inverse models. This paper reviews all approaches and highlights their potential and current limitations. These observational methods combined with models will support future endeavors in fine-scale GHG emission monitoring in cities and allow for validation of upcoming remote-sensing products of urban-scale GHG emissions.