Methods for easily following the main changes in the composition, stability, and acidity of bio-oil as a result of hydrotreatment are presented in this paper. The methods provide the basis for the development of an analytical protocol, which can be used for bio-oil, as well as the hydrotreated products from bio-oil. The correlation to more conventional methods is provided; however, the use of these methods for the upgrading products is different than previously recognized. The differences in the properties of bio-oil and the hydrotreated products will also create challenges for the analytical protocol. Polar pyrolysis liquids and their hydrotreated products can be divided into five main groups with solvent fractionation, and the change in the proportions of the groups as a result of handling or processing is easy to follow. Over the past 10 years, this method has been successfully used for comparison of fast pyrolysis bio-oil quality and the changes during handling and storage and provides the basis of the analytical protocol presented in this paper. This paper describes the use of the method for characterization of bio-oil hydrotreatment products. A discussion of the use of gas chromatographic and spectroscopic methods is also included. In addition, fuel oil analyses suitable for fast pyrolysis bio-oils and hydrotreatment products are discussed.