High spatial resolution images taken by unmanned aerial vehicles (UAVs) have been shown to have the potential for monitoring agronomic and environmental variables. However, it is necessary to capture a large number of overlapped images that must be mosaicked together to produce a single and accurate ortho-image (also called an ortho-mosaicked image) representing the entire area of work. Thus, ground control points (GCPs) must be acquired to ensure the accuracy of the mosaicking process. UAV ortho-mosaics are becoming an important tool for early site-specific weed management (ESSWM), as the discrimination of small plants (crop and weeds) at early growth stages is subject to serious limitations using other types of remote platforms with coarse spatial resolutions, such as satellite or conventional aerial platforms. Small changes in flight altitude are crucial for low-altitude image acquisition because these variations can cause important differences in the spatial resolution of the ortho-images. Furthermore, a decrease of flying altitude reduces the area covered by each single overlapped image, which implies an increase of both the sequence of images and the complexity of the image mosaicking procedure to obtain an ortho-image covering the whole study area. This study was carried out in two wheat fields naturally infested by broad-leaved and grass weeds at a very early phenological stage. The geometric accuracy differences and crop line alignment among ortho-mosaics created from UAV image series were investigated while taking into account three different flight altitudes (30, 60 and 100 m) and a number of GCPs (from 11 to 45). The results did not show relevant differences in geo-referencing accuracy on the interval of altitudes studied. Similarly, the increase of the number of GCPs did not imply a relevant increase of geo-referencing accuracy. Therefore, the most important parameter to consider when choosing the flying altitude is the ortho-image spatial resolution required rather than the geo-referencing accuracy. Regarding the crop mis-alignment, the results showed that the overall errors were less than twice the spatial resolution, which did not break the crop line continuity at the studied spatial resolutions (pixels from 7.4 to 24.7 mm for 30, 60 and 100 m flying altitudes respectively) on the studied crop (early wheat). The results lead to the conclusion that a UAV flying at a range of 30 to 100 m altitude and using a moderate number of GCPs is able to generate ultra-high spatial resolution ortho-imagesortho-images with the geo-referencing accuracy required to map small weeds in wheat at a very early phenological stage. This is an ambitious agronomic objective that is being studied in a wide research program whose global aim is to create broad-leaved and grass weed maps in wheat crops for an effective ESSWM.