A method of conducting an amplification assay, comprising: (a) contacting a biological sample with a control amplification reagent and a target amplification reagent to form a reaction mixture, wherein the control amplification reagent is capable of taking part in a nucleic acid amplification reaction involving a highly conserved region of a control nucleic acid or a portion thereof, if present in the biological sample, and wherein the target amplification reagent is capable of taking part in a nucleic acid amplification reaction involving a target nucleic acid or a portion thereof, if present in the biological sample; wherein the control amplification reagent comprises amplification oligonucleotides for use in producing two or more detectably distinguishable control amplicons, each having a different length, wherein the two or more different length control amplicons form a size control ladder comprised of amplicons of increasing length; and wherein the control nucleic acid varies in less than 1/100 or 1/1000 members of a population; (b) subjecting the reaction mixture to amplification conditions to produce an amplification mixture, whereby a portion of the highly conserved region of the control nucleic acid and the target nucleic acid or portion thereof, if present, are amplified to produce a detectable control amplicon and a detectable target amplicon; (c) evaluating the amplification mixture to detect the amounts of each of the control amplicon and the target amplicon; and (d) comparing the amount of detected control amplicon with the amount of detected target amplicon to evaluate the amount and quality of the target nucleic acid or portion thereof and/or the highly conserved region of the control nucleic acid or portion thereof, present in the biological sample. (a) contacting a biological sample with a control amplification reagent and a target amplification reagent to form a reaction mixture, wherein the control amplification reagent is capable of taking part in a nucleic acid amplification reaction involving a highly conserved region of a control nucleic acid or a portion thereof, if present in the biological sample, and wherein the target amplification reagent is capable of taking part in a nucleic acid amplification reaction involving a target nucleic acid or a portion thereof, if present in the biological sample; wherein the control amplification reagent comprises amplification oligonucleotides for use in producing two or more detectably distinguishable control amplicons, each having a different length, wherein the two or more different length control amplicons form a size control ladder comprised of amplicons of increasing length; and wherein the control nucleic acid varies in less than 1/100 or 1/1000 members of a population; (b) subjecting the reaction mixture to amplification conditions to produce an amplification mixture, whereby a portion of the highly conserved region of the control nucleic acid and the target nucleic acid or portion thereof, if present, are amplified to produce a detectable control amplicon and a detectable target amplicon; (c) evaluating the amplification mixture to detect the amounts of each of the control amplicon and the target amplicon; and (d) comparing the amount of detected control amplicon with the amount of detected target amplicon to evaluate the amount and quality of the target nucleic acid or portion thereof and/or the highly conserved region of the control nucleic acid or portion thereof, present in the biological sample.