<span class="paragraphSection"><strong>Summary:</strong> Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present <span style="font-style:italic;">FoldAtlas</span>, a web interface for accessing raw and processed structural data across thousands of transcripts. <span style="font-style:italic;">FoldAtlas</span> allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide <span style="font-style:italic;">in silico</span> and <span style="font-style:italic;">in vivo</span> secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into <span style="font-style:italic;">FoldAtlas</span> are from a new high-depth Structure-seq data analysis in <span style="font-style:italic;">Arabidopsis thaliana</span>, released with this work.<strong>Availability and Implementation:</strong> The <span style="font-style:italic;">FoldAtlas</span> website can be accessed at <a href="http://www.foldatlas.com">www.foldatlas.com</a>. Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985.<strong>Contact:</strong><a href="mailto:'yiliang.ding@jic.ac.uk'">yiliang.ding@jic.ac.uk</a> or <a href="mailto:'matthew.norris@jic.ac.uk'">matthew.norris@jic.ac.uk</a>.<strong>Supplementary information:</strong>Supplementary dataSupplementary data are available at <span style="font-style:italic;">Bioinformatics</span> online.</span>