The cholinergic nucleus basalis of Meynert, which is important for memory functions, shows neuronal activation (‘up-phase’) during the early stages of Alzheimer’s disease and neurodegeneration (‘down-phase’) in later stages of Alzheimer’s disease. MicroRNA-132 (miR-132) and the transcription factor early growth response-1 (EGR1) were proposed as possible candidate molecules regulating such an up–down activity pattern of the nucleus basalis of Meynert during the course of Alzheimer’s disease, as they both show this up–down pattern of expression in the prefrontal cortex during the course of Alzheimer’s disease. Not only do these two molecules stimulate synaptic activity and plasticity, they are also involved in Alzheimer’s disease pathology and might, in addition, affect cholinergic function. In the nucleus basalis of Meynert, we investigated the expression of miR-132 and EGR1 along the entire course of Alzheimer’s disease. Forty-nine post-mortem nucleus basalis of Meynert samples were studied, ranging from non-demented controls (Braak stage = 0) to late Alzheimer’s disease patients (Braak stage = VI), and from clinical Reisberg scale 1 to 7. Each Braak stage contained seven samples, that were all well matched for confounding factors, i.e. age (range 58–91), sex, post-mortem delay, cerebrospinal fluid pH (as a measure for agonal state), APOE genotype, clock time of death, tissue fixation time, and tissue storage time. The alterations of these two molecules were studied over the course of Alzheimer’s disease in relation to the expression of 4G8-stained amyloid-β, hyperphosphorylated tau stained by antibody AT8, neuronal fibrillary tangles and neuropil threads stained by silver, and in relation to alterations in choline acetyltransferase. We found that the expression of miR-132 and EGR1 in the nucleus basalis of Meynert was quite stable during the early stages of Alzheimer’s disease and decreased significantly only during late Alzheimer’s disease stages. In addition, miR-132 and EGR1 showed a significant positive correlation with choline acetyltransferase expression (r = 0.49, P < 0.001 and r = 0.61, P < 0.001), while choline acetyltransferase expression showed a significantly negative correlation with hyperphosphorylated tau (r = −0.33, P = 0.021) but no correlation with 4G8-stained amyloid-β. From the functional changes of miR-132 and EGR1 along the course of Alzheimer’s disease we conclude: (i) that these two molecules may play a role in keeping the cholinergic function intact in early Alzheimer’s disease stages; and (ii) that these molecules may contribute to the late neurodegeneration of this cholinergic nucleus.