Method for weighing containers, in particular capsules, in a filling machine suitable to fill said containers with at least one product and comprising a feeding station of said containers, a plurality of operating stations (A, D, R) for carrying out operations on said containers, weighing means (G, T) for weighing said containers and moving means provided with a plurality of supports with respective seats for housing and moving said containers sequentially through said operating stations (A, D, R), said method comprising supplying said supports with said containers in said feeding station, carrying out operations on said containers by means of said operating stations (A, D, R), and weighing said containers by means of said weighing means (G, T) with a defined precision and accuracy, comprising: - selecting during the operation of said filling machine a checking period; - stopping in defined inhibition time intervals (T1, T2, T3) of said checking period said supplying with said containers so as to leave empty established supports of the moving means intended to be positioned in at least one of said operating stations (A, D, R) in a weighing time interval of said checking period during which a sample of containers taken from at least one further established support of the moving means is weighed on said weighing means (G, T); - decreasing during said weighing time interval a nominal operation speed of said filling machine in order to increase a weighing time so as to weigh with an increased accuracy and precision said sample of containers in said weighing means (G, T); - inhibiting in said weighing time interval the operation of said at least one of said operating stations (A, D, R) in order not to perturb said weighing with vibrations and/or accelerations and/or air flows and/or air turbulences generated in the operation by said at least one of said operating stations (A, D, R); and - weighing said sample of containers filled with said product, in particular by first weighing means of said weighing means, in said weighing time interval. - selecting during the operation of said filling machine a checking period; - stopping in defined inhibition time intervals (T1, T2, T3) of said checking period said supplying with said containers so as to leave empty established supports of the moving means intended to be positioned in at least one of said operating stations (A, D, R) in a weighing time interval of said checking period during which a sample of containers taken from at least one further established support of the moving means is weighed on said weighing means (G, T); - decreasing during said weighing time interval a nominal operation speed of said filling machine in order to increase a weighing time so as to weigh with an increased accuracy and precision said sample of containers in said weighing means (G, T); - inhibiting in said weighing time interval the operation of said at least one of said operating stations (A, D, R) in order not to perturb said weighing with vibrations and/or accelerations and/or air flows and/or air turbulences generated in the operation by said at least one of said operating stations (A, D, R); and - weighing said sample of containers filled with said product, in particular by first weighing means of said weighing means, in said weighing time interval.